Cel_aging_1: Cel_YA_1
In LBMC/wormRef: Nematode Reference Data For The RAPToR Package
Cel_aging_1 R Documentation
Cel_YA_1
Description
Transcriptomic data from C. elegans aging adults/ rrf-3 mutants .
Usage
Cel_aging_1
Format
An object of class list of length 7.
Details
One (unpublished) time series is included in this dataset.
Byrne et al.
The gene expression matrix is log(X + 1) of quantile-normalized raw data,
filtered to keep genes with a strong aging signal.
Format
A list with :
-
$g: The gene expression matrix (genes as rows, samples as columns)
-
$p: A dataframe of phenotypic data on the samples, usually :
-
sname : The sample names (and colnames of the gene expression matrix).
-
age : Sample developmental age. May be scaled to join multiple datasets.
-
cov : A factor separating the samples into groups if needed (e.g multiple datasets, batches); else NULL.
-
age_ini : Sample chronological age, as given in the literature.
-
accession : Sample accession ID for GEO/ArrayExpress.
-
$geim_params: A list of elements needed for the gene expression interpolation model :
-
$formula : the model formula.
-
$method : the model type (eg. gam, glm).
-
$dim_red : the dimension reduction method to use (pca, ica).
-
$nc: The number PCA/ICA components to use in the model.
-
$t.unit: the time series unit (e.g 'hours').
-
$cov.levels: a named list of potential covariate with the level to interpolate as.
-
$metadata: a named list of extra metadata (e.g organism, profiling technology).
Source
References
\insertAllCited
LBMC/wormRef documentation built on April 6, 2023, 12:31 p.m.
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| Cel_aging_1 | R Documentation |
Cel_YA_1
Description
Transcriptomic data from C. elegans aging adults/ rrf-3 mutants .
Usage
Cel_aging_1
Format
An object of class list of length 7.
Details
One (unpublished) time series is included in this dataset.
Byrne et al.
The gene expression matrix is log(X + 1) of quantile-normalized raw data,
filtered to keep genes with a strong aging signal.
Format
A list with :
-
$g: The gene expression matrix (genes as rows, samples as columns) -
$p: A dataframe of phenotypic data on the samples, usually :-
sname: The sample names (and colnames of the gene expression matrix). -
age: Sample developmental age. May be scaled to join multiple datasets. -
cov: A factor separating the samples into groups if needed (e.g multiple datasets, batches); else NULL. -
age_ini: Sample chronological age, as given in the literature. -
accession: Sample accession ID for GEO/ArrayExpress.
-
-
$geim_params: A list of elements needed for the gene expression interpolation model :-
$formula: the model formula. -
$method: the model type (eg. gam, glm). -
$dim_red: the dimension reduction method to use (pca, ica). -
$nc: The number PCA/ICA components to use in the model.
-
-
$t.unit: the time series unit (e.g 'hours'). -
$cov.levels: a named list of potential covariate with the level to interpolate as. -
$metadata: a named list of extra metadata (e.g organism, profiling technology).
Source
References
\insertAllCitedR Package Documentation
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We want your feedback!
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